Friday, July 12, 2013

Java jar files - FatJar

http://fjep.sourceforge.net/#inst


The Fat Jar Eclipse Plug-In is a Deployment-Tool which deploys an Eclipse java-project into one executable jar.

It adds the Entry "Build Fat-JAR" to the Export-Wizard.
In addition to the eclipse standard jar-exporter referenced classes and jars are included to the "Fat-Jar", so the resulting jar contains all needed classes and can be executed directly with "java -jar", no classpath has to be set, no additional jars have to be deployed.

Jars, External-Jars, User-Libraries, System-Libraries, Classes-Folders and Project-Exports are considered by the plugin.
The Main-Class can be selected and Manifest-files are merged.
The One-JAR option integrates a specialised Class-Loader written by Simon Tuffs ( http://one-jar.sourceforge.net/ ) which handles jar-files inside a jar.
Individual files and folders can be excluded or added to the jar.
Different settings can be stored and re-executed as "Quick Build" via the context-menu.

Or

JARS=$(echo ${LIB_DIR}/* | tr ' ' ':')

java -classpath $JARS org.HelloWorld


Or

in Linux (Java 1.6 and above)

java -cp ".:../lib/*" org.HelloWorld


Maven shaded plugin

Junior / Senior Bioinformatician

http://bioinformatics.ca/node/17199

Institution/Company: 
Harvard School of Public Health
Location: 
Boston, MA, US
Job Description: 
*About us*
Harvard NeuroDiscovery serves neuroscientists from across the Harvard Medical School community and beyond, providing a range of core facilities, research platforms and funding opportunities to investigators that seek to understand the nervous system and to use that understanding to reduce disease burden. We embrace the broad spectrum of neurobiological investigation, from the most fundamental research, through applied translational research. We also promote a more collaborative biomedical neuroscience research community.  For more information, please visit www.neurodiscovery.harvard.edu.
As part of a new initiative, Harvard NeuroDiscovery is partnering with the Harvard School of Public Health’s Bioinformatics Core (HBC, http://compbio.sph.harvard.edu/chb)
to provide support in computational biology to our community

Institution/Company: 
Harvard School of Public Health
Location: 
Boston, MA, US
Job Description: 
*About us*
Harvard NeuroDiscovery serves neuroscientists from across the Harvard Medical School community and beyond, providing a range of core facilities, research platforms and funding opportunities to investigators that seek to understand the nervous system and to use that understanding to reduce disease burden. We embrace the broad spectrum of neurobiological investigation, from the most fundamental research, through applied translational research. We also promote a more collaborative biomedical neuroscience research community.  For more information, please visit www.neurodiscovery.harvard.edu.
As part of a new initiative, Harvard NeuroDiscovery is partnering with the Harvard School of Public Health’s Bioinformatics Core (HBC, http://compbio.sph.harvard.edu/chb)
to provide support in computational biology to our community

Linked - Albert-László Barabási







Linked,how everything is connected to everything else and what it means for business, science, and everyday life
Albert-László Barabási
Release Date: 2003-01-01
No. of Pages: 308
ISBN-10: 0452284392
ISBN-13: 9780452284395

Description:
A cocktail party. A terrorist cell. Ancient bacteria. An international conglomerate. All are networks, and all are a part of a surprising scientific revolution. Albert-Laszlo Barabasi, the nations foremost expert in the new science of networks, takes us on an intellectual adventure to prove that social networks, corporations, and living organisms are more similar than previoulsy thought. Grasping a full understanding of network science, will someday allow us to design blue chip businesses, stop the outbreak of deadly diseases, and influence the exchange of ideas and information. Just as James Gleick brought the discovery of the Chaos theory to the general public, Linked tells the story of the true science of the future.

http://en.wikipedia.org/wiki/Albert-L%C3%A1szl%C3%B3_Barab%C3%A1si

Best known for his work on network theory

Finding Simple Tests for Brain Disorders Turns Out to Be Complex

http://www.wbur.org/npr/198086616/MENTAL-ILLNESS-BIOMARKERS

Thursday, July 11, 2013

Tuesday, July 9, 2013

Debug hibernate

production-data-source.xml <property name="show_sql">true</property>
hibernate.cfg.xml  <property name="show_sql">true</property>

Saturday, July 6, 2013

Poems, Karuta

Impassionate gods have never seen such Tatsuta River, crimson that flows above, the water below.

http://onethousandsummers.blogspot.ca/2012/07/ogura-hyakunin-isshu-poem-17-ariwara-no.html

Friday, July 5, 2013

A Disease Without a Cure Spreads Quietly in the West

http://www.nytimes.com/2013/07/05/health/a-disease-without-a-cure-spreads-quietly-in-the-west.html?hp&_r=0

Coccidioidomycosis, known as “cocci,” is an insidious airborne fungal disease in which microscopic spores in the soil take flight on the wind or even a mild breeze to lodge in the moist habitat of the lungs and, in the most extreme instances, spread to the bones, the skin, the eyes or, in Mr. Klorman’s case, the brain.

Mutational heterogeneity in cancer and the search for new cancer-associated genes

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12213.html

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer1, 2, 3, 4, 5,6, 7, 8, 9. These studies involve the sequencing of matched tumour–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour–normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Thursday, July 4, 2013

The Lions

http://vancouverhiking.tripod.com/id10.html
http://www.trailcafe.com/hiking/individual/lion_heads.html
http://www.clubtread.com/routes/Route.aspx?Route=239 

6 BEST CAR-FREE HIKES IN VANCOUVER

http://vancouverist.info/6-car-free-hikes-in-vancouver/


1. Hanes Valley Traverse
2. Whyte Lake/ Eagle Bluffs Lookout
3. Mosquito Creek Cascades/Mt. Fromme Summit
4. Diez Vistas or Lindsay Lake Loop
5. Mt. Gardner on Bowen Island
6. Norvan Falls/ Coliseum/Lynn Peak/Lynn Lake/The Needles